yacrd usable for Nanopore cDNA reads?

[michieitel]

Hi!

I am wondering if I can use ycard on my set of ONT cDNA reads that were generated using the SQK-PCS109 PCR-cDNA Sequencing Kit?
Will it remove rare splice variants?
Thanks for your thoughts on this.

Michael

[natir]

Hi,

First, you want use yacrd for detect chimeric read or perform scrubbing ?

I test yacrd to detect chimeric reads on cDNA data one time for on a read that we already thought was chimeric, and it worked but I think more test are require to generalize.

I think that yacrd can be used on cDNA data by carefully choosing the parameters of minimap2 and yacrd and if we accept that an alternative transcript containing an additional exon sequenced only one time is considered a chimera by yacrd. But you can use yacrd to get read they are probably chimeric and run a second analysis after to separate rare splice variants and chimeric reads.

If you need help to found best parameter and separated the chimeras to rare splice variants. Don't hesitate to ask me.

Pierre

[michieitel]

Hi Piere,

thanks for your comments.

I want to use it for scrubbing of reads before piping them into an error correction tool to further improve read quality and genome mapping accuracy.

I think that yacrd can be used on cDNA data by carefully choosing the parameters of minimap2 and yacrd and if we accept that an alternative transcript containing an additional exon sequenced only one time is considered a chimera by yacrd. But you can use yacrd to get read they are probably chimeric and run a second analysis after to separate rare splice variants and chimeric reads.

That is a great idea. I will give it a try and get back to you in case I am encountering issues.
cheers
Michael